A Simple Protocol for Informative Visualization of Enriched Gene Ontology Terms

Abstract

In genome-scale datasets, Gene Ontology (GO) enrichment is a common analysis to highlight functions over-represented or under-represented in a subset of differentially expressed genes to elucidate the biological significance of the results. However, despite the diversity of existing tools to analyze GO enrichment, it is often difficult to integrate results in an article figure with sufficient clarity. This is partly due to the high number and to the redundancy of the enriched GO terms, especially when looking at large sets of differentially expressed genes. Here, we provide a simple method to plot representative enriched GO terms. The list of representative enriched GO terms is obtained using existing tools Panther and REVIGO and results are represented in different plots generated from a homemade R script and the ggplot2 R package. The generated plots are publication-quality figures. The diversity of represented parameters makes the plots highly informative (number of genes associated with the enriched GO terms, fold enrichment and level of statistical significance). Comparison of GO enrichment between different lists of genes in a single plot is possible. As proof of concept, we performed this analysis on an Arabidopsis heat responsive transcriptome dataset recently published.